<div dir="ltr">Wow, nice going, Tiago. Will buy!<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <span dir="ltr"><<a href="mailto:tra@popgen.net" target="_blank">tra@popgen.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
<br>
I would like to announce "Bioinformatics with Python Cookbook" which I<br>
authored. As you might imagine Biopython is discussed heavily in the<br>
book.<br>
<br>
This book is slightly different from the standard books on<br>
Bioinformatics and Python. It is not about teaching Bioinformatics<br>
algorithms, but about solving practical day-to-day problems with<br>
Python, for example:<br>
<br>
Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with<br>
filtering of datasets.<br>
<br>
Genomics: processing reference genomes of both high-quality references<br>
of model species and low-quality non-model species. Also discussed are<br>
genome annotations and gene ontologies.<br>
<br>
Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...<br>
<br>
Genome simulation: mostly forward-time simulations, but also a bit of<br>
coalescent<br>
<br>
Phylogenetics: tree reconstruction and tree drawing<br>
<br>
Proteins: PDB processing and visualization.<br>
<br>
Other topics like processing map data, GBIF, interfacing with<br>
Cytoscape, accessing lots of online databases, ...<br>
<br>
There is a bit on interacting with R/Bioconductor via Python.<br>
<br>
Finally we discuss high-performance in Python: faster algorithms,<br>
clusters, Numba and Cython. Also related technologies like Docker<br>
<br>
The book discusses the usual Python Libraries in the field: Biopython,<br>
PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries<br>
like NumPy, SciPy, matplotlib and scikit-learn.<br>
<br>
The code is fully available for free at github<br>
<a href="https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb" rel="noreferrer" target="_blank">https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb</a><br>
<br>
I am keen on maintaining the book code, so if you find any issues<br>
please do contact me.<br>
<br>
The book is available in the usual places (Amazon, etc.) in paperback<br>
and e-book format. The web page of the book is<br>
<a href="https://www.packtpub.com/application-development/bioinformatics-python-cookbook" rel="noreferrer" target="_blank">https://www.packtpub.com/application-development/bioinformatics-python-cookbook</a><br>
<br>
Regards,<br>
Tiago<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">Iddo Friedberg<br><a href="http://iddo-friedberg.net/contact.html" target="_blank">http://iddo-friedberg.net/contact.html</a><br>++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>>>----.<--.>++++++.<<<<------------------------------------.<br></div>
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